We analyzed responses of chironomid (Diptera:Chironomidae) communities to environmental factors in 124 natural, moderately, and highly disturbed springs in the Italian Prealps and Alps to investigate environmental factors influencing species distribution in springs and to evaluate chironomids as bioindicators of spring water quality. Self-Organizing Map analysis found differences among spring types and effects of anthropogenic pressures. Natural or little-disturbed springs at high altitude with low temperature, low conductivity, and high current velocity differed from lowland springs, including highly disturbed ones, with low current velocity and higher temperature, conductivity, and nutrient concentrations. Cold stenothermal intolerant species were clustered in the 1st group, tolerant and euriecious species in the 2nd group. Indicator value analysis detected species characterizing springs with different degrees of disturbance and of different types. Most species’ distributions were related to water temperature and conductivity. Coinertia Analysis (CoA) detected relationships among species structure and environmental variables. CoA axis 1 represented a gradient of water temperature, altitude, alkalinity, and conductivity and separated cold stenothermal species (Pseudokiefferiella parva, Pseudodiamesa branickii, Diamesa spp.) from species tolerant of high temperatures (Polypedilum nubeculosum, Phaenopsectra flavipes, Paratrissocladius excerptus). Axis 2 represented a hydrologic (rheocrene–limnocrene) and anthropogenic disturbance (total disturbance, agriculture, organic debris) gradient and separated species by preference for water velocity and spring type (rheocrenes: Eukiefferiella spp.; limnocrenes: Prodiamesa olivacea, Natarsia sp.), and pollution tolerance (P. nubeculosum, Macropelopia spp.). Water temperature and chemical composition affected chironomid distribution. Some species were associated with degraded (P. nubeculosum) or pristine conditions (Diamesa spp., Stilocladius montanus).